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jmchilton · Apr 2, 2024 · 13fbd4f · 13fbd4f
1 parent c253a99
commit 13fbd4f
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Showing 14 changed files with 688 additions and 8 deletions.
diff --git a/client/src/api/datasetCollections.ts b/client/src/api/datasetCollections.ts
@@ -1,4 +1,4 @@
-import { CollectionEntry, DCESummary, HDCADetailed, isHDCA } from "@/api";
+import { CollectionEntry, DCESummary, HDCADetailed, HDCASummary, isHDCA } from "@/api";
 import { fetcher } from "@/api/schema";
 
 const DEFAULT_LIMIT = 50;
@@ -11,7 +11,16 @@ const getCollectionDetails = fetcher.path("/api/dataset_collections/{id}").metho
  */
 export async function fetchCollectionDetails(params: { id: string }): Promise<HDCADetailed> {
     const { data } = await getCollectionDetails({ id: params.id });
-    return data;
+    return data as HDCADetailed;
+}
+
+/**
+ * Fetches the details of a collection.
+ * @param params.id The ID of the collection (HDCA) to fetch.
+ */
+export async function fetchCollectionSummary(params: { id: string }): Promise<HDCASummary> {
+    const { data } = await getCollectionDetails({ id: params.id, view: "collection" });
+    return data as HDCASummary;
 }
 
 const getCollectionContents = fetcher

diff --git a/client/src/api/histories.ts b/client/src/api/histories.ts
@@ -12,3 +12,5 @@ export const updateHistoryItemsInBulk = fetcher
     .path("/api/histories/{history_id}/contents/bulk")
     .method("put")
     .create();
+export const sharing = fetcher.path("/api/histories/{history_id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/histories/{history_id}/enable_link_access").method("put").create();
diff --git a/client/src/api/jobs.ts b/client/src/api/jobs.ts
@@ -2,6 +2,8 @@ import { components, fetcher } from "@/api/schema";
 
 export type JobDestinationParams = components["schemas"]["JobDestinationParams"];
 
+export const getJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
+
 export const jobLockStatus = fetcher.path("/api/job_lock").method("get").create();
 export const jobLockUpdate = fetcher.path("/api/job_lock").method("put").create();
 

diff --git a/client/src/api/workflows.ts b/client/src/api/workflows.ts
@@ -3,3 +3,6 @@ import { fetcher } from "@/api/schema";
 export const workflowsFetcher = fetcher.path("/api/workflows").method("get").create();
 
 export const invocationCountsFetcher = fetcher.path("/api/workflows/{workflow_id}/counts").method("get").create();
+
+export const sharing = fetcher.path("/api/workflows/{workflow_id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/workflows/{workflow_id}/enable_link_access").method("put").create();
diff --git a/client/src/components/Markdown/parse.ts b/client/src/components/Markdown/parse.ts
@@ -160,6 +160,7 @@ export function getArgs(content: string): GalaxyDirectiveSection {
     };
 }
 
+
 function namedArgumentRegex(argument: string): RegExp {
     return new RegExp(`(\\s*${argument}\\s*=)` + FUNCTION_ARGUMENT_VALUE_REGEX);
 }
@@ -168,3 +169,48 @@ function namedArgumentRegex(argument: string): RegExp {
 function escapeRegExpReplacement(value: string): string {
     return value.replace(/\$/g, "$$$$");
 }
+
+class ReferencedObjects {
+    jobs: Set<string> = new Set();
+    historyDatasets: Set<string> = new Set();
+    historyDatasetCollections: Set<string> = new Set();
+    workflows: Set<string> = new Set();
+    invocations: Set<string> = new Set();
+}
+
+export function referencedObjects(markdown: string) {
+    const { sections } = splitMarkdown(markdown);
+    const objects = new ReferencedObjects();
+    for (const section of sections) {
+        if (!("args" in section)) {
+            continue;
+        }
+        const args = section.args;
+        if (!args) {
+            continue;
+        }
+        if ("job_id" in args) {
+            addToSetIfHasValue(args.job_id, objects.jobs);
+        }
+        if ("history_dataset_id" in args) {
+            addToSetIfHasValue(args.history_dataset_id, objects.historyDatasets);
+        }
+        if ("history_dataset_collection_id" in args) {
+            addToSetIfHasValue(args.history_dataset_collection_id, objects.historyDatasetCollections);
+        }
+        if ("invocation_id" in args) {
+            addToSetIfHasValue(args.invocation_id, objects.invocations);
+        }
+        if ("workflow_id" in args) {
+            addToSetIfHasValue(args.workflow_id, objects.workflows);
+        }
+        // TODO: implicit collect job ids
+    }
+    return objects;
+}
+
+function addToSetIfHasValue(value: string | undefined, toSet: Set<string>): void {
+    if (value) {
+        toSet.add(value);
+    }
+}